development roadmap (initial public version, to be amended)

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Nov 14, 2008, 1:33:54 PM11/14/08
This roadmap comes with no release dates. However, it is safe to
assume that each numbered point requires two weeks to complete.

1. In results files, implement absolute chromosome coordinates
(instead of TSS-relative coordinates)

2. Provide full-genome-sequence search option as an addition to
existing functionality

3. Implement "TFBS enrichment analysis" for promoters; in the simplest
form, this will be an ad hoc promoters scoring scheme; this should
noticeably ease the selection of targets for experimental verification

4. Improve tasks management: add an ability to descriptively name the
tasks being submitted, and to retrieve (and delete?) previous results

5. Enable public (API/GET/web-service) access to internal COTRASIF
database of promoters, for all genomes; make dumps available

6. Implement automatic calculation of the PWM threshold (similar to
how it is done for HMM); this will be an additional feature - manual
input of threshold will be possible

7. Improve conservation filter: a) allow users to specify %id and
orthology types for filtering, b) introduce position-constrained
filtering (with distance measured from the TSS of each of the
orthologous genes); consider implementing multi-species (as opposed to
two-species) filtering

8. New development roadmap will be needed here. As a preview: a)
include nucleosome position prediction as an additional filter, b)
integrate Gene Ontology enrichment analysis (Fisher exact test,
hypergeometric test, Bayesian), c) add plant genomes database to the
Cotrasif import pipeline, to make plant genomes available for search.

As a permanent "background" task - increase the number of genomes
available for search; we've just

+ added Ciona intestinalis genome - almost 700 protein-coding genes
with transcript status = 'KNOWN'

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